The general analysis path would be:
1 - Map the transcripts to a reference genome to obtain location coordinates. One option is BLAST, which has a wrapper in the Tool Shed See http://galaxyproject.org/wiki/Tool%20Shed
2 - Import known protein-coding and non-protein coding tracks. See "Get Data"
3 - Use an intersection query to identify overlapping regions between the datasets to obtain annotation See "Operate on Genomic Intervals"
The first mapping step would require a local or cloud instance, the other steps can be done within the public Galaxy or your own. Help: http://galaxyproject.org/wiki/Admin/Get%20Galaxy
Best wishes for your project!
Jen Galaxy team
On 9/29/11 9:35 AM, dongdong zhaoweiming wrote:
Hi, I want to evaluate wherther my assembly transcripts produced by trinity is protein-coding or notcoding. I found two methods which are "txCdsPredict" program from the UCSC(John R Prensner,2011) and Codon Substitution Frequencies,CSF(Michael F. Lin,2008). I wonder if galaxy can do this? Thanks a lot! weimin zhao
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